Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006189.1 Hibiscus syriacus cultivar Beakdansim tig00014728_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 980383
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 5 of 7
Found at i:532012 original size:21 final size:21
Alignment explanation
Indices: 531986--532027 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
531976 TGAGCTATGG
*
531986 CTTTGAAGTAAGACGCCTTGA
1 CTTTGAAGTAAAACGCCTTGA
*
532007 CTTTGAAGTAAAACTCCTTGA
1 CTTTGAAGTAAAACGCCTTGA
532028 TTCTTAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (21 bp):
CTTTGAAGTAAAACGCCTTGA
Found at i:535438 original size:23 final size:23
Alignment explanation
Indices: 535408--535456 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
535398 TGGTGGTTGG
*
535408 TTTAATGG-ATGTTTAAACTTTAT
1 TTTAATGGTATATTT-AACTTTAT
*
535431 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
535454 TTT
1 TTT
535457 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:547838 original size:44 final size:45
Alignment explanation
Indices: 547732--547856 Score: 173
Period size: 46 Copynumber: 2.8 Consensus size: 45
547722 TATAAAATTT
* * *
547732 CTTATCATTTATCCCATAAGCTCATAAGCTTATTTTACCACAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCACAATA
*
547777 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTATCA-ATATA
1 CTTACCATTT-ATTCCATAAGCTCGTAAGCTTATTTTACCACA-ATA
*
547823 CTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
547857 GCATGCTTAC
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
44 25 0.34
45 12 0.16
46 36 0.49
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCACAATA
Found at i:548005 original size:40 final size:40
Alignment explanation
Indices: 547961--548110 Score: 273
Period size: 40 Copynumber: 3.8 Consensus size: 40
547951 ACCGTAGTGC
547961 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
548001 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
548041 TACACATAAGGTCGTGCCCACCATATACACCCAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
548081 TATACATAAGGTCGTGCCCACCATGTACAC
1 TACACATAAGGTCGTGCCCACCATATACAC
548111 TTAGTGTCTT
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 107 1.00
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:550464 original size:2 final size:2
Alignment explanation
Indices: 550457--550483 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
550447 TCGTAACAGC
550457 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
550484 AGAGTTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:553322 original size:26 final size:26
Alignment explanation
Indices: 553287--553337 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
553277 CCAGAAGGTG
*
553287 CGCTGACTAGATCTTCTAGAAACTGT
1 CGCTGACTAGACCTTCTAGAAACTGT
553313 CGCTGACTAGACCTTCTAGAAACTG
1 CGCTGACTAGACCTTCTAGAAACTG
553338 CCAAGTTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (26 bp):
CGCTGACTAGACCTTCTAGAAACTGT
Found at i:567352 original size:5 final size:5
Alignment explanation
Indices: 567338--567385 Score: 62
Period size: 5 Copynumber: 9.6 Consensus size: 5
567328 TTGCTCAATC
* *
567338 AAAAT GAAAT AAAAT AAAAT AAAGT AAAAT AAAAT AATAA- AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAA
567386 CAATGGTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 2 0.05
5 33 0.89
6 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:570236 original size:18 final size:18
Alignment explanation
Indices: 570215--570250 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
570205 GGAGATTTTG
*
570215 GTAAAATGAGATTAAATA
1 GTAAAAAGAGATTAAATA
*
570233 GTAAAAAGATATTAAATA
1 GTAAAAAGAGATTAAATA
570251 AATAAAGGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (18 bp):
GTAAAAAGAGATTAAATA
Found at i:574089 original size:43 final size:43
Alignment explanation
Indices: 573999--574089 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
573989 GATTAACCTT
** *
573999 TTAGTCTAAACGACATCACATTGTAGCAAAAAATGTTATTTCT
1 TTAGTCTAAACGACATCACATTGTAGCAAAAAATGTTATGCCC
*
574042 TTAGTCTAAACGACATCACCTTGTAGCAAAAAATGTT-TGCCAC
1 TTAGTCTAAACGACATCACATTGTAGCAAAAAATGTTATGCC-C
574085 TTAGT
1 TTAGT
574090 GAATTAATAG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 2 0.05
43 41 0.95
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (43 bp):
TTAGTCTAAACGACATCACATTGTAGCAAAAAATGTTATGCCC
Found at i:582411 original size:11 final size:12
Alignment explanation
Indices: 582384--582412 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
582374 AGTTGTTATG
582384 TTGGGCTAGGTT
1 TTGGGCTAGGTT
582396 TTGGGCTAGG-T
1 TTGGGCTAGGTT
582407 TTGGGC
1 TTGGGC
582413 CATCTATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.07, C:0.10, G:0.45, T:0.38
Consensus pattern (12 bp):
TTGGGCTAGGTT
Found at i:582465 original size:6 final size:6
Alignment explanation
Indices: 582454--582539 Score: 83
Period size: 6 Copynumber: 14.8 Consensus size: 6
582444 GAAATAAAGG
* *
582454 GAAAAT GAAAAT -AAAATT AAAAAT -AAAAT GAAAAT GAAAAT AAAAAT
1 GAAAAT GAAAAT GAAAA-T GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT
* *
582501 -AAAACT GAAAAT GAAAAT AAAAAT AAAAAT -AAAA- GAAAA
1 GAAAA-T GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAA
582540 ATAGGTAGAT
Statistics
Matches: 72, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
5 21 0.29
6 43 0.60
7 8 0.11
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.16
Consensus pattern (6 bp):
GAAAAT
Found at i:582487 original size:18 final size:17
Alignment explanation
Indices: 582454--582541 Score: 95
Period size: 18 Copynumber: 5.0 Consensus size: 17
582444 GAAATAAAGG
*
582454 GAAAATGAAAATAAAATT
1 GAAAAT-AAAATAAAAAT
* *
582472 AAAAATAAAATGAAAAT
1 GAAAATAAAATAAAAAT
*
582489 GAAAATAAAAATAAAACT
1 GAAAAT-AAAATAAAAAT
582507 GAAAATGAAAATAAAAAT
1 GAAAAT-AAAATAAAAAT
* *
582525 AAAAATAAAAGAAAAAT
1 GAAAATAAAATAAAAAT
582542 AGGTAGATAA
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
17 24 0.41
18 35 0.59
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.17
Consensus pattern (17 bp):
GAAAATAAAATAAAAAT
Found at i:582499 original size:24 final size:23
Alignment explanation
Indices: 582455--582528 Score: 123
Period size: 24 Copynumber: 3.2 Consensus size: 23
582445 AAATAAAGGG
582455 AAAATGAAAAT-AAAATTAAAAAT
1 AAAATGAAAATGAAAA-TAAAAAT
582478 AAAATGAAAATGAAAATAAAAAT
1 AAAATGAAAATGAAAATAAAAAT
582501 AAAACTGAAAATGAAAATAAAAAT
1 AAAA-TGAAAATGAAAATAAAAAT
582525 AAAA
1 AAAA
582529 ATAAAAGAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
23 22 0.45
24 27 0.55
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (23 bp):
AAAATGAAAATGAAAATAAAAAT
Found at i:589415 original size:18 final size:18
Alignment explanation
Indices: 589392--589434 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
589382 AAATTGTTTT
589392 AAATAAAAGATAAGGATA
1 AAATAAAAGATAAGGATA
* *
589410 AAATAAAAGATAATGATG
1 AAATAAAAGATAAGGATA
589428 AAATAAA
1 AAATAAA
589435 TAAATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.14, T:0.19
Consensus pattern (18 bp):
AAATAAAAGATAAGGATA
Found at i:590246 original size:20 final size:21
Alignment explanation
Indices: 590213--590251 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
590203 AATAAGGAAA
590213 AGATAATTCGTAAA-ATAAAG
1 AGATAATTCGTAAAGATAAAG
590233 AGATAATT-GCTAAAGATAA
1 AGATAATTCG-TAAAGATAA
590252 TTCTTAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.06
20 12 0.71
21 4 0.24
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.26
Consensus pattern (21 bp):
AGATAATTCGTAAAGATAAAG
Found at i:598414 original size:90 final size:90
Alignment explanation
Indices: 598293--598470 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
598283 TAATCCCGAA
* * * * *
598293 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCATGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCATAATATGAC
598358 TAGGATAACTTGGATATAAAAGGAT
66 TAGGATAACTTGGATATAAAAGGAT
*
598383 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCATAATATGAC
* *
598448 TAGGGTAACTTGGCTATAAAAGG
66 TAGGATAACTTGGATATAAAAGG
598471 GTGTGTTAGG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCATAATATGAC
TAGGATAACTTGGATATAAAAGGAT
Found at i:604839 original size:90 final size:90
Alignment explanation
Indices: 604717--604894 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 90
604707 TAATCCCGAA
* * * * *
604717 TATTTAATTTCAATTAAGTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTCCAATTAAGTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
604782 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
604807 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAAGTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
604872 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
604895 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.36
Consensus pattern (90 bp):
TATTAAATTCCAATTAAGTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
TAGGGTAACTTGGATATAAAAGGAT
Found at i:606930 original size:74 final size:74
Alignment explanation
Indices: 606833--606971 Score: 233
Period size: 74 Copynumber: 1.9 Consensus size: 74
606823 AGGGCAATTG
* * * *
606833 CCCCTCCCAACTTTGATGGTCTAATTATATTTTAGGTCATTGATAATTATAAAATCATTATAATT
1 CCCCTCCCAACTTTAATGATCTAATTACATTTTAGGTCACTGATAATTATAAAATCATTATAATT
606898 AAGTTTTTA
66 AAGTTTTTA
*
606907 CCCCTCTCAACTTTAATGATCTAATTACATTTTAGGTCACTGATAATTATAAAATCATTATAATT
1 CCCCTCCCAACTTTAATGATCTAATTACATTTTAGGTCACTGATAATTATAAAATCATTATAATT
606972 GAGCCCTTGT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 60 1.00
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.42
Consensus pattern (74 bp):
CCCCTCCCAACTTTAATGATCTAATTACATTTTAGGTCACTGATAATTATAAAATCATTATAATT
AAGTTTTTA
Found at i:607387 original size:20 final size:20
Alignment explanation
Indices: 607362--607427 Score: 123
Period size: 20 Copynumber: 3.3 Consensus size: 20
607352 AAGAGAAGAG
*
607362 AAGCACTTACCCATTCGACT
1 AAGCACTTACCCATTGGACT
607382 AAGCACTTACCCATTGGACT
1 AAGCACTTACCCATTGGACT
607402 AAGCACTTACCCATTGGACT
1 AAGCACTTACCCATTGGACT
607422 AAGCAC
1 AAGCAC
607428 AATATTGAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.23
Consensus pattern (20 bp):
AAGCACTTACCCATTGGACT
Found at i:612568 original size:29 final size:30
Alignment explanation
Indices: 612524--612581 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
612514 ATTTTTTTTA
*
612524 AAAAAAAGACCCT-AAATTTTCTAAAATATT
1 AAAAAAAGACCATAAAATTTT-TAAAATATT
612554 AAAAAAA-ACCATAAAATTTTTAAAATAT
1 AAAAAAAGACCATAAAATTTTTAAAATAT
612582 CATAAAACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (30 bp):
AAAAAAAGACCATAAAATTTTTAAAATATT
Found at i:612597 original size:29 final size:29
Alignment explanation
Indices: 612524--612606 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
612514 ATTTTTTTTA
* *
612524 AAAAAAAGACCCTAAATTTTCTAAAATATT
1 AAAAAAA-ACCCTAAATTTTATAAAATATC
*
612554 AAAAAAAACCATAAAATTTT-TAAAATATC
1 AAAAAAAACCCT-AAATTTTATAAAATATC
* **
612583 ATAAAACCCCCTAAATTTTATAAA
1 AAAAAAAACCCTAAATTTTATAAA
612607 CCCCCAAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 7 0.16
29 24 0.53
30 14 0.31
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.29
Consensus pattern (29 bp):
AAAAAAAACCCTAAATTTTATAAAATATC
Found at i:620057 original size:31 final size:31
Alignment explanation
Indices: 620010--620078 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
620000 TTGTAGATCT
620010 TCAACGAGACCTCAGAGAATTTGTTTAGTCTA
1 TCAA-GAGACCTCAGAGAATTTGTTTAGTCTA
* *
620042 TCAAGAGGCCTCAGAGAATTTGTTTAGTTTA
1 TCAAGAGACCTCAGAGAATTTGTTTAGTCTA
620073 TCAAGA
1 TCAAGA
620079 ACCCAAGTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (31 bp):
TCAAGAGACCTCAGAGAATTTGTTTAGTCTA
Found at i:632722 original size:18 final size:19
Alignment explanation
Indices: 632692--632727 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
632682 TTAGGAACTC
632692 ATATTTGTCTAATTTTAAA
1 ATATTTGTCTAATTTTAAA
632711 ATATTT-TCTAATTTTAA
1 ATATTTGTCTAATTTTAA
632728 CAGGACAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.56
Consensus pattern (19 bp):
ATATTTGTCTAATTTTAAA
Found at i:632928 original size:19 final size:19
Alignment explanation
Indices: 632913--632953 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
632903 ATCTTTTCTT
632913 AAAA-TCATTTTATTTTTC
1 AAAATTCATTTTATTTTTC
632931 AAAATTCATTTT-TGTTTTC
1 AAAATTCATTTTAT-TTTTC
632950 AAAA
1 AAAA
632954 GAATTCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (19 bp):
AAAATTCATTTTATTTTTC
Found at i:636280 original size:18 final size:18
Alignment explanation
Indices: 636257--636299 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
636247 CTTTAATTTA
*
636257 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
636275 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
636293 TTTATTT
1 TTTATTT
636300 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:636732 original size:21 final size:21
Alignment explanation
Indices: 636708--636750 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
636698 AAACACTTTG
636708 AGAA-AAGAGAAAAAGATAAGA
1 AGAACAAGA-AAAAAGATAAGA
* *
636729 AGAACAAGAAAAGAGATCAGA
1 AGAACAAGAAAAAAGATAAGA
636750 A
1 A
636751 ACAGAATAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.67, C:0.05, G:0.23, T:0.05
Consensus pattern (21 bp):
AGAACAAGAAAAAAGATAAGA
Found at i:639804 original size:22 final size:20
Alignment explanation
Indices: 639772--639827 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
639762 CCGAAAGGGG
* *
639772 GTATCGGTACCATAGTATGGTA
1 GTATCGATACCATAGTA-AG-A
*
639794 GTATCGATACCATGGTAAGA
1 GTATCGATACCATAGTAAGA
639814 GTATCGATACCATA
1 GTATCGATACCATA
639828 CAACATCGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 14 0.47
21 1 0.03
22 15 0.50
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (20 bp):
GTATCGATACCATAGTAAGA
Found at i:639810 original size:17 final size:18
Alignment explanation
Indices: 639788--639826 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
639778 GTACCATAGT
639788 ATGGT-AGTATCGATACC
1 ATGGTAAGTATCGATACC
639805 ATGGTAAGAGTATCGATACC
1 ATGGT-A-AGTATCGATACC
639825 AT
1 AT
639827 ACAACATCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
20 14 0.74
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (18 bp):
ATGGTAAGTATCGATACC
Found at i:639821 original size:95 final size:94
Alignment explanation
Indices: 639695--639883 Score: 283
Period size: 95 Copynumber: 2.0 Consensus size: 94
639685 ATACTAACGA
* *
639695 GGTAGTATCGATACCATGGTAAGGGTATCGATACC-TGGA-AACATCGAATCTAAAATTGGTATC
1 GGTAGTATCGATACCATGGTAAGAGTATCGATACCAT--ACAACATCGAAGCTAAAATTGGTATC
* *
639758 TATACCGAAAGGGGGTATCGGTACCATAGTAT
64 GATACC-AAAGGGGGTATCAGTACCATAGTAT
*
639790 GGTAGTATCGATACCATGGTAAGAGTATCGATACCATACAACATCGAAGCTAAAATTGGTATGGA
1 GGTAGTATCGATACCATGGTAAGAGTATCGATACCATACAACATCGAAGCTAAAATTGGTATCGA
*
639855 TACCAGAGGGGGTATCAGTACCATAGTAT
66 TACCAAAGGGGGTATCAGTACCATAGTAT
639884 AGAAGTATTT
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
94 24 0.28
95 61 0.71
96 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (94 bp):
GGTAGTATCGATACCATGGTAAGAGTATCGATACCATACAACATCGAAGCTAAAATTGGTATCGA
TACCAAAGGGGGTATCAGTACCATAGTAT
Found at i:639917 original size:94 final size:95
Alignment explanation
Indices: 639698--639917 Score: 259
Period size: 95 Copynumber: 2.3 Consensus size: 95
639688 CTAACGAGGT
* * * *
639698 AGTATCGATACCATGGTAAGGGTATCGATACC-TGGA-AACATCGAATCTAAAATTGGTATCTAT
1 AGTATCGATACCAGGGTAAGAGTATCGATACCAT--ACAACATCGAAGCTAAAATTGGTATCGAT
* * *
639761 ACCGAAAGGGGGTATCGGTACCATAGTATGGT
64 ACCGAAAGGGGGTATCAGTACCATAGTATAGA
* *
639793 AGTATCGATACCATGGTAAGAGTATCGATACCATACAACATCGAAGCTAAAATTGGTATGGATAC
1 AGTATCGATACCAGGGTAAGAGTATCGATACCATACAACATCGAAGCTAAAATTGGTATCGATAC
*
639858 C-AGAGGGGGTATCAGTACCATAGTATAGA
66 CGAAAGGGGGTATCAGTACCATAGTATAGA
*** *
639887 AGTATTTTTACTAGGGT-AGTAGTATCGATAC
1 AGTATCGATACCAGGGTAAG-AGTATCGATAC
639918 TATTGAGCTT
Statistics
Matches: 109, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
93 2 0.02
94 48 0.44
95 58 0.53
96 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (95 bp):
AGTATCGATACCAGGGTAAGAGTATCGATACCATACAACATCGAAGCTAAAATTGGTATCGATAC
CGAAAGGGGGTATCAGTACCATAGTATAGA
Found at i:640593 original size:45 final size:45
Alignment explanation
Indices: 640293--640582 Score: 483
Period size: 45 Copynumber: 6.4 Consensus size: 45
640283 TGAAAATAAT
* *
640293 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGA
1 AATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
*
640338 AATGTATATGGGTACATTATCAACAGAAAAGTATCCTATAGTTGA
1 AATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
*
640383 AATGTATATGGGTACATTATCAAAAGAAAAGTATGCTATAGTTGA
1 AATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
* *
640428 AATGTATATGGGTACATTATCAACAGAAAAGTATGTTATAGTTAA
1 AATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
640473 AATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
1 AATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
*
640518 AATGTATATGGGTACATTATCAACAGAAAAGTATG-TCATAGCTGA
1 AATGTATATGGGTACATTATCAACAGAAAAGTATGCT-ATAGTTGA
* *
640563 AATGCATATGGGTGCATTAT
1 AATGTATATGGGTACATTAT
640583 TGGCATAAAA
Statistics
Matches: 231, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
44 1 0.00
45 230 1.00
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (45 bp):
AATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
Found at i:641322 original size:2 final size:2
Alignment explanation
Indices: 641315--641366 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
641305 TGAAGAGATG
641315 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
641357 AT AT AT AT AT
1 AT AT AT AT AT
641367 GTACAACAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:643167 original size:2 final size:2
Alignment explanation
Indices: 643160--643186 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
643150 ATTAGGTCAG
643160 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
643187 GTTGTTATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:645185 original size:94 final size:93
Alignment explanation
Indices: 645024--645221 Score: 290
Period size: 94 Copynumber: 2.1 Consensus size: 93
645014 ATACCGATGA
* * * *
645024 GGTAGTATCGATACCATGGTAAGGGTATCGATACCTGGAAACATCGAATCTAAAATTGGTATCGA
1 GGTAGTATCGATAACATGGTAAGAGTATCGATACCT-GAAACATCGAAGCTAAAATTGGAATCGA
*
645089 TACCGGAAGGGGTATCGGTACCATAGTAT
65 TACCAGAAGGGGTATCGGTACCATAGTAT
645118 GGTAGTATCGATAACATGGTAAGAGTATCGATACCAT-ACAACATCGAAGCTAAAATTGGAATCG
1 GGTAGTATCGATAACATGGTAAGAGTATCGATACC-TGA-AACATCGAAGCTAAAATTGGAATCG
*
645182 ATACCAGAAGGGGTATCGGTATCATAGTAT
64 ATACCAGAAGGGGTATCGGTACCATAGTAT
* *
645212 AGAAGTATCG
1 GGTAGTATCG
645222 GTACTAGGAT
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
93 1 0.01
94 92 0.98
95 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (93 bp):
GGTAGTATCGATAACATGGTAAGAGTATCGATACCTGAAACATCGAAGCTAAAATTGGAATCGAT
ACCAGAAGGGGTATCGGTACCATAGTAT
Found at i:645238 original size:20 final size:20
Alignment explanation
Indices: 645194--645247 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
645184 ACCAGAAGGG
*
645194 GTATCGGTATCATAGTATAGAA
1 GTATCGGTA-C-TAGGATAGAA
*
645216 GTATCGGTACTAGGATAGTA
1 GTATCGGTACTAGGATAGAA
*
645236 GTATCGATACTA
1 GTATCGGTACTA
645248 TTGAGCTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 19 0.66
21 1 0.03
22 9 0.31
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.31
Consensus pattern (20 bp):
GTATCGGTACTAGGATAGAA
Found at i:646044 original size:45 final size:45
Alignment explanation
Indices: 645654--646033 Score: 636
Period size: 45 Copynumber: 8.4 Consensus size: 45
645644 TGAAAATAAT
* * *
645654 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGT
1 AATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
645699 AATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
1 AATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
*
645744 AATGTATATGGGTACATTATCAACATAAAAGTATGCTATAGTTGA
1 AATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
*
645789 AATGTATATGAGTACATTATCAACAGAAAAGTATGCTATAGTTGA
1 AATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
* *
645834 AATGTACATGGGTACATTATGAACAGAAAAGTATGCTATAGTTGA
1 AATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
* *
645879 AATGTATATGGGTACATTATCAACAGAAAAGTATGTTATAGTTAA
1 AATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
645924 AATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
1 AATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
*
645969 AATGTATATGGGTACATTATCAACAGAAAAGTATG-TCATAGCTGA
1 AATGTATATGGGTACATTATCAACAGAAAAGTATGCT-ATAGTTGA
* *
646014 AATGCATATGGGTGCATTAT
1 AATGTATATGGGTACATTAT
646034 TGGCATAAAA
Statistics
Matches: 316, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
44 1 0.00
45 315 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.31
Consensus pattern (45 bp):
AATGTATATGGGTACATTATCAACAGAAAAGTATGCTATAGTTGA
Found at i:646057 original size:34 final size:34
Alignment explanation
Indices: 646014--646078 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
646004 TCATAGCTGA
*
646014 AATGCATATGGGTGCATTATTGGCATAAAAGAAT
1 AATGCATATGAGTGCATTATTGGCATAAAAGAAT
*
646048 AATGCATATGAGTGCATTATTGGCATGAAAG
1 AATGCATATGAGTGCATTATTGGCATAAAAG
646079 GATGCCATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.29
Consensus pattern (34 bp):
AATGCATATGAGTGCATTATTGGCATAAAAGAAT
Found at i:646774 original size:2 final size:2
Alignment explanation
Indices: 646767--646794 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
646757 TGAAGGGATG
646767 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
646795 TGTACAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:650385 original size:15 final size:15
Alignment explanation
Indices: 650367--650419 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
650357 TTTAGCGAAC
650367 TTTATTTTCA-TTAAA
1 TTTATTTT-ATTTAAA
*
650382 TTTATTTTATTTTAA
1 TTTATTTTATTTAAA
*
650397 TTTATTTTACTTT-AT
1 TTTATTTTA-TTTAAA
650412 TTTATTTT
1 TTTATTTT
650420 TCTCTGAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 1 0.03
15 30 0.88
16 3 0.09
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTTTATTTAAA
Found at i:650392 original size:5 final size:5
Alignment explanation
Indices: 650382--650419 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
650372 TTTCATTAAA
* *
650382 TTTAT TTTAT TTTAA TTTAT TTTAC TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
650420 TCTCTGAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:650400 original size:10 final size:10
Alignment explanation
Indices: 650367--650415 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
650357 TTTAGCGAAC
*
650367 TTTATTTTCA
1 TTTATTTTAA
* * *
650377 TTAAATTTAT
1 TTTATTTTAA
650387 TTTATTTTAA
1 TTTATTTTAA
*
650397 TTTATTTTAC
1 TTTATTTTAA
650407 TTTATTTTA
1 TTTATTTTA
650416 TTTTTCTCTG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATTTTAA
Found at i:654917 original size:18 final size:18
Alignment explanation
Indices: 654881--654920 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
654871 CTTTAATTTA
*
654881 TTTATTTAATCATTTTCT
1 TTTATTTAATCATTATCT
654899 TTTATTTAATTC-TTATCT
1 TTTATTTAA-TCATTATCT
654917 TTTA
1 TTTA
654921 AAAAAACAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATTTAATCATTATCT
Found at i:664760 original size:14 final size:14
Alignment explanation
Indices: 664738--664790 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
664728 TCGATTATAT
*
664738 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
664752 GTTCATTTA---T-
1 GTTCATTTATGTTC
664762 GTTCATTTATGTTC
1 GTTCATTTATGTTC
664776 GTTCATTTATGTTC
1 GTTCATTTATGTTC
664790 G
1 G
664791 AACAGATGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 23 0.68
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:664770 original size:24 final size:24
Alignment explanation
Indices: 664725--664789 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 24
664715 CGTTCGTGAA
*
664725 CGTTCGATTATATGTTCGTTTATGTT
1 CGTTC-ATT-TATGTTCATTTATGTT
664751 CGTTCATTTATGTTCATTTATGTT
1 CGTTCATTTATGTTCATTTATGTT
664775 CGTTCATTTATGTTC
1 CGTTCATTTATGTTC
664790 GAACAGATGA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
24 30 0.79
25 3 0.08
26 5 0.13
ACGTcount: A:0.15, C:0.14, G:0.15, T:0.55
Consensus pattern (24 bp):
CGTTCATTTATGTTCATTTATGTT
Found at i:665065 original size:10 final size:10
Alignment explanation
Indices: 665052--665092 Score: 55
Period size: 10 Copynumber: 3.8 Consensus size: 10
665042 TTGTTTGTGT
665052 TGTTCGTTTA
1 TGTTCGTTTA
665062 TGTTCGTTTA
1 TGTTCGTTTA
665072 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
665085 TGTTCGTT
1 TGTTCGTT
665093 CGTTATTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 18 0.64
13 10 0.36
ACGTcount: A:0.07, C:0.10, G:0.22, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:665070 original size:23 final size:22
Alignment explanation
Indices: 665044--665109 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 22
665034 GTTTTTTTTT
665044 GTTTGTGTTGTTCGTTTATGTTC
1 GTTTGT-TTGTTCGTTTATGTTC
*
665067 GTTTATTGTGTTCGTTTATGTTC
1 GTTTGTT-TGTTCGTTTATGTTC
*
665090 GTTCGTTATTGTTCGTTTAT
1 GTTTG-T-TTGTTCGTTTAT
665110 TTATTAAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 1 0.03
23 23 0.62
24 12 0.32
25 1 0.03
ACGTcount: A:0.08, C:0.09, G:0.23, T:0.61
Consensus pattern (22 bp):
GTTTGTTTGTTCGTTTATGTTC
Found at i:665196 original size:16 final size:16
Alignment explanation
Indices: 665175--665207 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
665165 AAAAAAATTT
665175 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
665191 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
665207 T
1 T
665208 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:665958 original size:12 final size:12
Alignment explanation
Indices: 665941--666004 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
665931 AATAAGCTCG
*
665941 TTTATCGACTCA
1 TTTATCAACTCA
665953 TTTATCAACTCA
1 TTTATCAACTCA
*
665965 TTTAT-AAGCTCG
1 TTTATCAA-CTCA
* *
665977 TTTA-CTGATTCA
1 TTTATC-AACTCA
*
665989 TTTATAAACTCA
1 TTTATCAACTCA
666001 TTTA
1 TTTA
666005 CTGGGTTCTC
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
11 2 0.05
12 37 0.93
13 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.45
Consensus pattern (12 bp):
TTTATCAACTCA
Found at i:665979 original size:36 final size:36
Alignment explanation
Indices: 665932--666004 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 36
665922 ATGTTCATGA
*
665932 ATAAGCTCGTTTA-TCGACTCATTTATCAACTCATTT
1 ATAAGCTCGTTTACT-GACTCATTTATAAACTCATTT
*
665968 ATAAGCTCGTTTACTGATTCATTTATAAACTCATTT
1 ATAAGCTCGTTTACTGACTCATTTATAAACTCATTT
666004 A
1 A
666005 CTGGGTTCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 33 0.97
37 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.42
Consensus pattern (36 bp):
ATAAGCTCGTTTACTGACTCATTTATAAACTCATTT
Found at i:665989 original size:24 final size:24
Alignment explanation
Indices: 665962--666007 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
665952 ATTTATCAAC
* *
665962 TCATTTATAAGCTCGTTTACTGAT
1 TCATTTATAAACTCATTTACTGAT
665986 TCATTTATAAACTCATTTACTG
1 TCATTTATAAACTCATTTACTG
666008 GGTTCTCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (24 bp):
TCATTTATAAACTCATTTACTGAT
Found at i:684683 original size:52 final size:53
Alignment explanation
Indices: 684579--684683 Score: 140
Period size: 55 Copynumber: 2.0 Consensus size: 53
684569 ACATTCAAAT
*
684579 GATTCATGAAGAAGAAAATCCGATGAATGAAGAAATTTGAACCTGATTGAAGAAC
1 GATTCATGAAGAAGAAAATCCGATGAATGAAG--ATTTGAACCTGATCGAAGAAC
* * **
684634 GATTCATGAAGAAGGACATCCGATGAATGAAG-TTTGAAGTTGATCGAAGA
1 GATTCATGAAGAAGAAAATCCGATGAATGAAGATTTGAACCTGATCGAAGA
684684 CTTCTTTCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
52 15 0.33
55 30 0.67
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.23
Consensus pattern (53 bp):
GATTCATGAAGAAGAAAATCCGATGAATGAAGATTTGAACCTGATCGAAGAAC
Found at i:685028 original size:6 final size:6
Alignment explanation
Indices: 685017--685053 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
685007 ATTAACACCT
685017 TTTGCA TTTGCA TTTGACA TTTGCA TTTGCA -TTGCA T
1 TTTGCA TTTGCA TTTG-CA TTTGCA TTTGCA TTTGCA T
685054 AAGCATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.17
6 18 0.62
7 6 0.21
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (6 bp):
TTTGCA
Found at i:685039 original size:13 final size:12
Alignment explanation
Indices: 685017--685053 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 12
685007 ATTAACACCT
685017 TTTGCATTTGCA
1 TTTGCATTTGCA
685029 TTTGACATTTGCA
1 TTTG-CATTTGCA
685042 TTTGCA-TTGCA
1 TTTGCATTTGCA
685053 T
1 T
685054 AAGCATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 6 0.25
12 6 0.25
13 12 0.50
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (12 bp):
TTTGCATTTGCA
Found at i:688274 original size:123 final size:124
Alignment explanation
Indices: 688055--688306 Score: 337
Period size: 123 Copynumber: 2.0 Consensus size: 124
688045 ATTGGAGAAA
* * * * * *
688055 AAGAATAAGCGGTGCCAGAACATGAAGCATTCCGGGATCTCGAATCAAACGGTCCTAGAGATCGG
1 AAGAATAAGCGATGCCAGAACATGAAGCATTCCGCGATCTAGAAGCAAACGGTCCAAGAGATCAG
* * * * *
688120 AATGGATGAAGAGAGAAATTATAATATTTTC-TTGTGACGTTGTCAGTAACCCGTCAGG
66 AATGGATGAAGAGAGAAATTATAATATTTTCTTTGTGAAGTTATCAATAACCCATCAAG
* * *
688178 AAGAATAAGCGATGCCAGAACATGAAGCATTCTGCGATCTAGAAGCAGATGGTCCAAGAGATCAG
1 AAGAATAAGCGATGCCAGAACATGAAGCATTCCGCGATCTAGAAGCAAACGGTCCAAGAGATCAG
* *
688243 AATGGATGAAGGATAGAAATTGTAATA-TTTCTTTGTGAAGTTATCAATAACCCATCAAG
66 AATGGATGAA-GAGAGAAATTATAATATTTTCTTTGTGAAGTTATCAATAACCCATCAAG
688302 AAGAA
1 AAGAA
688307 GAGGACCTCA
Statistics
Matches: 111, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
123 70 0.63
124 41 0.37
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.23
Consensus pattern (124 bp):
AAGAATAAGCGATGCCAGAACATGAAGCATTCCGCGATCTAGAAGCAAACGGTCCAAGAGATCAG
AATGGATGAAGAGAGAAATTATAATATTTTCTTTGTGAAGTTATCAATAACCCATCAAG
Found at i:688766 original size:124 final size:125
Alignment explanation
Indices: 688519--688766 Score: 435
Period size: 124 Copynumber: 2.0 Consensus size: 125
688509 TACACACGTT
688519 GGGGCATGACTGAACCCACATCACGTTGAGATGACAAGATTCAGACCAAGAAGGCATTGAGAATG
1 GGGGCATGACTGAACCCACATCACGTTGAGATGACAAGATTCAGACCAAGAAGGCATTGAGAATG
688584 AGCCTTACAATTTGAGGTGTTGGGGCACTTTGAAGGCCCATACCAGTACAAGATAATGTC
66 AGCCTTACAATTTGAGGTGTTGGGGCACTTTGAAGGCCCATACCAGTACAAGATAATGTC
* *
688644 GGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGGCATT-AGATTG
1 GGGGCATGACTGAACCCACATCACGTTGAGATGACAAGATTCAGACCAAGAAGGCATTGAGAATG
* ** *
688708 AGCCTTACAATTTGAGGTGTTGGGGCATTTTGAAGGCCTGTACCAGTATAAGATAATGT
66 AGCCTTACAATTTGAGGTGTTGGGGCACTTTGAAGGCCCATACCAGTACAAGATAATGT
688767 TGCGGCACTA
Statistics
Matches: 117, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
124 60 0.51
125 57 0.49
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (125 bp):
GGGGCATGACTGAACCCACATCACGTTGAGATGACAAGATTCAGACCAAGAAGGCATTGAGAATG
AGCCTTACAATTTGAGGTGTTGGGGCACTTTGAAGGCCCATACCAGTACAAGATAATGTC
Found at i:690271 original size:36 final size:36
Alignment explanation
Indices: 690071--690488 Score: 606
Period size: 36 Copynumber: 11.4 Consensus size: 36
690061 GGGGCAAAGT
690071 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA
* * *
690107 TCTATCCTAAGCCTTCACCGAAGAGTAGTGAAGTAAA
1 -CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA
*
690144 TCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGC-AA
1 -CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA
*
690180 CTCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCATAT
1 C-C-ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCA-AA
* * *
690219 CAATCTTAAGCATTCACCGAAGAGTAATGAAGCAAA
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA
*
690255 CCATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAAA
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA
* *
690291 CCATCTTAAGCCTTTACCGGAGAGTAGTGAAGCAAA
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA
* *
690327 CCATCTTAATCCTTCACCGGAGAGTAGTGAAGCAAA
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA
*
690363 CCATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAAA
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA
*
690399 CCATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAAA
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA
690435 CCATCTTAAGCCTTCACC-AGAGAGTAGTGAAGCAAA
1 CCATCTTAAGCCTTCACCGA-AGAGTAGTGAAGCAAA
*
690471 CTCATCTGTAAGTCTTCA
1 C-CATCT-TAAGCCTTCA
690489 GAGCAAGATG
Statistics
Matches: 352, Mismatches: 22, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
35 1 0.00
36 210 0.60
37 130 0.37
38 9 0.03
39 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (36 bp):
CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA
Found at i:690941 original size:13 final size:13
Alignment explanation
Indices: 690923--690947 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
690913 TGAAGCAAAC
690923 CCATCAGTAAGTG
1 CCATCAGTAAGTG
690936 CCATCAGTAAGT
1 CCATCAGTAAGT
690948 CTTTTGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:691002 original size:93 final size:93
Alignment explanation
Indices: 690842--691070 Score: 395
Period size: 93 Copynumber: 2.5 Consensus size: 93
690832 AGTCCTTCGG
* *
690842 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAGTTTGTAAGCCTTCACATAA
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACAGAA
*
690907 GAGTAGTGAAGCAAACCCATCAGTAAGT
66 GAGTAGTGAAGCAAACACATCAGTAAGT
*
690935 GCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACAGAA
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACAGAA
*
691000 GAGTAGTGAAGCAAATACATCAGTAAGT
66 GAGTAGTGAAGCAAACACATCAGTAAGT
* *
691028 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
691071 CCATCAGTAA
Statistics
Matches: 128, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 128 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (93 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACAGAA
GAGTAGTGAAGCAAACACATCAGTAAGT
Found at i:691097 original size:42 final size:42
Alignment explanation
Indices: 691028--691292 Score: 155
Period size: 42 Copynumber: 6.1 Consensus size: 42
691018 ATCAGTAAGT
*
691028 GCCATCAGTAAGTCTTTCGAGCATGATGA-TGAAGTCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGAGT-AAATCCTTCGG
* *
691070 GCCATCAGTAAGTCTTTTGAGCGTGATGAGTAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGAGTAAATCCTTCGG
** * * * * * *
691112 GTAAT-TGTAAGCCTTCACAGAAG-A-GTAGTGAAGCAAATCCATAAGTAAGT
1 GCCATCAGTAAGTCTT-TC-G-AGCATG-A-TG-AGTAAATCC-T---T-CGG
* *
691162 GCCATAAGTAAGTCTTTCGAGCATGATGA-TGAAGTCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGAGT-AAATCCTTCGG
* *
691204 GCTATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGAGTAAATCCTTCGG
* ** * * * * *
691246 GTCATTTGTGAGCCTTTCGAGCAAGATGA-TAAACCCATCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGAGTAAATCCTTCGG
*
691287 GTCATC
1 GCCATC
691293 CATAAGACCT
Statistics
Matches: 171, Mismatches: 35, Indels: 35
0.71 0.15 0.15
Matches are distributed among these distances:
41 23 0.13
42 101 0.59
43 5 0.03
44 4 0.02
45 8 0.05
46 2 0.01
47 6 0.04
48 4 0.02
49 4 0.02
50 6 0.04
51 8 0.05
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGAGTAAATCCTTCGG
Found at i:691168 original size:13 final size:13
Alignment explanation
Indices: 691150--691174 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
691140 TGAAGCAAAT
691150 CCATAAGTAAGTG
1 CCATAAGTAAGTG
691163 CCATAAGTAAGT
1 CCATAAGTAAGT
691175 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATAAGTAAGTG
Found at i:691176 original size:134 final size:134
Alignment explanation
Indices: 690935--691261 Score: 555
Period size: 134 Copynumber: 2.4 Consensus size: 134
690925 ATCAGTAAGT
690935 GCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACAGAA
1 GCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTAA-TTGTAAGCCTTCACAGAA
* *
691000 GAGTAGTGAAGCAAATACATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCC
65 GAGTAGTGAAGCAAATACATAAGTAAGTGCCATAAGTAAGTCTTTCGAGCATGATGATGAAGTCC
691065 TTCGG
130 TTCGG
* *
691070 GCCATCAGTAAGTCTTTTGAGCGTGATGAGTAAATCCTTCGGGTAATTGTAAGCCTTCACAGAAG
1 GCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTAATTGTAAGCCTTCACAGAAG
*
691135 AGTAGTGAAGCAAATCCATAAGTAAGTGCCATAAGTAAGTCTTTCGAGCATGATGATGAAGTCCT
66 AGTAGTGAAGCAAATACATAAGTAAGTGCCATAAGTAAGTCTTTCGAGCATGATGATGAAGTCCT
691200 TCGG
131 TCGG
* * * *
691204 GCTATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATTTGTGAGCCTT
1 GCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGT-AATTGTAAGCCTT
691262 TCGAGCAAGA
Statistics
Matches: 180, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
134 125 0.69
135 55 0.31
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (134 bp):
GCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTAATTGTAAGCCTTCACAGAAG
AGTAGTGAAGCAAATACATAAGTAAGTGCCATAAGTAAGTCTTTCGAGCATGATGATGAAGTCCT
TCGG
Found at i:691202 original size:22 final size:22
Alignment explanation
Indices: 691171--691244 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 22
691161 TGCCATAAGT
*
691171 AAGTCTTTCGAGCATGATGATG
1 AAGTCCTTCGAGCATGATGATG
* *
691193 AAGTCCTTCGGGC-T-ATCA-G
1 AAGTCCTTCGAGCATGATGATG
* *
691212 TAAGTCTTTCGAGCATGATGATT
1 -AAGTCCTTCGAGCATGATGATG
*
691235 AAATCCTTCG
1 AAGTCCTTCG
691245 GGTCATTTGT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
19 1 0.03
20 14 0.36
21 2 0.05
22 22 0.56
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (22 bp):
AAGTCCTTCGAGCATGATGATG
Found at i:691619 original size:54 final size:54
Alignment explanation
Indices: 691555--691833 Score: 425
Period size: 54 Copynumber: 5.2 Consensus size: 54
691545 AGAATCACAC
691555 CAGAAGATTGTTCGAGTTCCCACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCCCACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGG
* *
691609 CAGAAGATTGTTCGAGTTCCCACTCCCTAAAGAAAGAGAGAGCAAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCCCACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGG
* * *
691663 AAGAAGATTGTTCGAGTTCCCACTCCCTAAAGAAAGAGGAAGCGAACTCGTAGG
1 CAGAAGATTGTTCGAGTTCCCACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGG
* **
691717 GAGAAGATTGTTCGAGTTCCCACTCCCTAAAGAAAGAGGGAGCGAACCCGTTCG
1 CAGAAGATTGTTCGAGTTCCCACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGG
* * ** *
691771 TAGAAGATTGTTCGAGTT-CTACTCCCTAAAAGAAAGAGGGAATGAACCCGTTGG
1 CAGAAGATTGTTCGAGTTCCCACTCCCT-AAAGAAAGAGGGAGCGAACCCGTAGG
691825 CAGAAGATT
1 CAGAAGATT
691834 TTTCAAGTCT
Statistics
Matches: 206, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
53 8 0.04
54 198 0.96
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (54 bp):
CAGAAGATTGTTCGAGTTCCCACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGG
Found at i:696799 original size:3 final size:3
Alignment explanation
Indices: 696791--696819 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
696781 TGTGGATAGG
696791 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
696820 AGCTGTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:698406 original size:30 final size:30
Alignment explanation
Indices: 698372--698439 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
698362 TTAGTCCTTA
698372 AGCTTCAACTATAAACACCTTAGCTCATTT
1 AGCTTCAACTATAAACACCTTAGCTCATTT
698402 AGCTTCAACTATAAACACCTTAGCTCATTT
1 AGCTTCAACTATAAACACCTTAGCTCATTT
698432 AGCTTCAA
1 AGCTTCAA
698440 AATCATCCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.34, C:0.26, G:0.07, T:0.32
Consensus pattern (30 bp):
AGCTTCAACTATAAACACCTTAGCTCATTT
Found at i:706635 original size:63 final size:63
Alignment explanation
Indices: 706536--706663 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
706526 AGAATCATTC
706536 ATGGTGGCAAATTATGGCATACTCTAAATCTCCTACATAAGTCTGCCATATCCTTTGGCTATT
1 ATGGTGGCAAATTATGGCATACTCTAAATCTCCTACATAAGTCTGCCATATCCTTTGGCTATT
706599 ATGGTGGCAAATTATGGCATACTCTAAATCTCCTACATAAGTCTGCCATATCCTTTGGCTATT
1 ATGGTGGCAAATTATGGCATACTCTAAATCTCCTACATAAGTCTGCCATATCCTTTGGCTATT
706662 AT
1 AT
706664 ACAATCATAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (63 bp):
ATGGTGGCAAATTATGGCATACTCTAAATCTCCTACATAAGTCTGCCATATCCTTTGGCTATT
Found at i:709204 original size:15 final size:15
Alignment explanation
Indices: 709186--709215 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
709176 AAAAGTAAAT
709186 CATAAAAAAACTTAA
1 CATAAAAAAACTTAA
*
709201 CATAAAAAGACTTAA
1 CATAAAAAAACTTAA
709216 TACTTACTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.13, G:0.03, T:0.20
Consensus pattern (15 bp):
CATAAAAAAACTTAA
Found at i:709408 original size:12 final size:11
Alignment explanation
Indices: 709386--709411 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
709376 GAGTTTTAAG
709386 AAATTAAAAAA
1 AAATTAAAAAA
709397 AAATTAAAAAA
1 AAATTAAAAAA
709408 AAAT
1 AAAT
709412 AATAGAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAATTAAAAAA
Found at i:709525 original size:15 final size:15
Alignment explanation
Indices: 709506--709535 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
709496 TATTTATAGG
709506 ATTTTTTATA-ATTT
1 ATTTTTTATACATTT
709520 ATTTTTTATACATTT
1 ATTTTTTATACATTT
709535 A
1 A
709536 AAAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTTTATACATTT
Found at i:710492 original size:14 final size:14
Alignment explanation
Indices: 710473--710499 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
710463 TATGAGTTGA
710473 ATTCATACATACAC
1 ATTCATACATACAC
710487 ATTCATACATACA
1 ATTCATACATACA
710500 TGCATTAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (14 bp):
ATTCATACATACAC
Found at i:715385 original size:20 final size:21
Alignment explanation
Indices: 715334--715385 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
715324 CTGTTGAAGA
*
715334 GGTATCGATA-CTGTAAGGGT
1 GGTATCGATACCTGTAAGGAT
*
715354 AGTATCGATACCTG-AAGGAT
1 GGTATCGATACCTGTAAGGAT
715374 GGTATCGATACC
1 GGTATCGATACC
715386 CTTAAAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (21 bp):
GGTATCGATACCTGTAAGGAT
Found at i:715439 original size:54 final size:53
Alignment explanation
Indices: 715355--715496 Score: 167
Period size: 54 Copynumber: 2.6 Consensus size: 53
715345 TGTAAGGGTA
715355 GTATCGATACCTGAAGGATGGTATCGATACCCTTAAAACATCGAATGCCAGATTG
1 GTATCGATACCTG-AGGA-GGTATCGATACCCTTAAAACATCGAATGCCAGATTG
* * * **
715410 GTATCGATACCTTGAGGAGGTATCGATACCCTTGAAACATCGAATTCTATTTTG
1 GTATCGATACC-TGAGGAGGTATCGATACCCTTAAAACATCGAATGCCAGATTG
* * * *
715464 GTATCGGTATCATGAGAATGTATCGATACCCTT
1 GTATCGATA-CCTGAGGAGGTATCGATACCCTT
715497 GAAGGGAAGT
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
54 58 0.76
55 16 0.21
56 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (53 bp):
GTATCGATACCTGAGGAGGTATCGATACCCTTAAAACATCGAATGCCAGATTG
Found at i:716106 original size:23 final size:23
Alignment explanation
Indices: 716076--716165 Score: 116
Period size: 23 Copynumber: 4.0 Consensus size: 23
716066 TTCGGGACAA
716076 ATATGTGGCACTTCGGTGCAAAT
1 ATATGTGGCACTTCGGTGCAAAT
*
716099 ATATGTGGCACTTCGGTGCAAAC
1 ATATGTGGCACTTCGGTGCAAAT
*
716122 CTATGTGGTC-CTTCGG-G-ACAAT
1 ATATGTGG-CACTTCGGTGCA-AAT
716144 -TATGTGGCACTTCGGTGCAAAT
1 ATATGTGGCACTTCGGTGCAAAT
716166 TACGAGCTGT
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
20 1 0.02
21 14 0.24
22 7 0.12
23 36 0.61
24 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (23 bp):
ATATGTGGCACTTCGGTGCAAAT
Found at i:716621 original size:20 final size:20
Alignment explanation
Indices: 716584--716623 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
716574 CCTTTTGGTA
*
716584 TTTATGTAAATTATTATGTT
1 TTTATGTAAATAATTATGTT
716604 TTTATGTAAA-AATGTATGTT
1 TTTATGTAAATAAT-TATGTT
716624 AAATGGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (20 bp):
TTTATGTAAATAATTATGTT
Found at i:717480 original size:15 final size:15
Alignment explanation
Indices: 717430--717492 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 15
717420 CTACCATTAC
*
717430 CTCCACCACCATCAT
1 CTCCACCACCACCAT
* * * * *
717445 CTTCACTACTATCAC
1 CTCCACCACCACCAT
717460 CTCCACCACCACCAT
1 CTCCACCACCACCAT
*
717475 CTCCACCGCCACCAT
1 CTCCACCACCACCAT
717490 CTC
1 CTC
717493 AGCTAGATCA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.24, C:0.54, G:0.02, T:0.21
Consensus pattern (15 bp):
CTCCACCACCACCAT
Found at i:721261 original size:31 final size:31
Alignment explanation
Indices: 721214--721284 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
721204 TTGTTAAAAA
*
721214 TAGATGTCTAACGTTTTTTTCGTTACACTTT
1 TAGATGTCTAACGTTTTCTTCGTTACACTTT
* * *
721245 TAGGTGTCTAATGTTTTCTTCGTTACATTTT
1 TAGATGTCTAACGTTTTCTTCGTTACACTTT
721276 TAGATGTCT
1 TAGATGTCT
721285 GGTCCGTTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.18, C:0.14, G:0.15, T:0.52
Consensus pattern (31 bp):
TAGATGTCTAACGTTTTCTTCGTTACACTTT
Found at i:721397 original size:19 final size:19
Alignment explanation
Indices: 721373--721415 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
721363 TACTTTTTTC
721373 TAAAA-TATTAAAAAATCCA
1 TAAAATTATTAAAAAAT-CA
* *
721392 TAAAATTTTTAAAATATCA
1 TAAAATTATTAAAAAATCA
721411 TAAAA
1 TAAAA
721416 CCCCCTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATTATTAAAAAATCA
Found at i:722005 original size:14 final size:14
Alignment explanation
Indices: 721986--722033 Score: 96
Period size: 14 Copynumber: 3.4 Consensus size: 14
721976 GAGGGATGAT
721986 CGACAATGGAGGTC
1 CGACAATGGAGGTC
722000 CGACAATGGAGGTC
1 CGACAATGGAGGTC
722014 CGACAATGGAGGTC
1 CGACAATGGAGGTC
722028 CGACAA
1 CGACAA
722034 CGGGTGGGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.31, C:0.23, G:0.33, T:0.12
Consensus pattern (14 bp):
CGACAATGGAGGTC
Found at i:732221 original size:3 final size:3
Alignment explanation
Indices: 732213--732239 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
732203 GTATATTCTT
732213 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
732240 TATTACTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:735900 original size:4 final size:4
Alignment explanation
Indices: 735891--736949 Score: 2051
Period size: 4 Copynumber: 266.2 Consensus size: 4
735881 TTTAAAGATT
735891 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
735939 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
735987 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736035 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736083 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736131 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736179 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736227 TACA TACA TACA TAC- -ACA TACA TAC- -ACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736271 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736319 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736367 TACA TACA TACA TACA TAC- TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736414 TACA TAC- TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736461 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736509 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736557 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736605 TACA TACA T-CA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736652 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736700 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736748 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736796 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
736844 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
736892 TACA TACA TACA TACC TACA TACA TACA TACA TACA TACA TACA TACAA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC-A
736941 TACA TACA T
1 TACA TACA T
736950 TGATTGTATT
Statistics
Matches: 1045, Mismatches: 2, Indels: 16
0.98 0.00 0.02
Matches are distributed among these distances:
2 4 0.00
3 9 0.01
4 1028 0.98
5 4 0.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:740056 original size:25 final size:25
Alignment explanation
Indices: 740028--740083 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
740018 ACCATGCTCA
*
740028 TATAAAT-TGCACCGAAGTGCCAACG
1 TATAAATATGCACCGAAGTACC-ACG
*
740053 TAT-AATATGTACCGAAGTACCACG
1 TATAAATATGCACCGAAGTACCACG
*
740077 TAGAAAT
1 TATAAAT
740084 GTCCCAAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (25 bp):
TATAAATATGCACCGAAGTACCACG
Found at i:740097 original size:23 final size:23
Alignment explanation
Indices: 740050--740195 Score: 132
Period size: 23 Copynumber: 6.3 Consensus size: 23
740040 CGAAGTGCCA
* * *
740050 ACGTATAATATGTACCGAAGTACC
1 ACGTAGAA-ATGTCCCGAAGGACC
*
740074 ACGTAGAAATGTCCCAAAGGACC
1 ACGTAGAAATGTCCCGAAGGACC
* *
740097 ACATAGATATGTCCCG-AGGACC
1 ACGTAGAAATGTCCCGAAGGACC
* *
740119 GCGTAGAAATGTCTCGAAGGACC
1 ACGTAGAAATGTCCCGAAGGACC
* * **
740142 ACGTAGAATTTTTTCGAAGGACC
1 ACGTAGAAATGTCCCGAAGGACC
* * *
740165 GCGTATAATTGTCCCGAAGGACC
1 ACGTAGAAATGTCCCGAAGGACC
*
740188 GCGTAGAA
1 ACGTAGAA
740196 CCCTCGACTC
Statistics
Matches: 100, Mismatches: 21, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
22 18 0.18
23 75 0.75
24 7 0.07
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.21
Consensus pattern (23 bp):
ACGTAGAAATGTCCCGAAGGACC
Found at i:740125 original size:45 final size:46
Alignment explanation
Indices: 740057--740148 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 46
740047 CCAACGTATA
*
740057 ATATGTACCGAAGTACCACGTAGAAATGTCCCAAAGGACCACATAG
1 ATATGTACCGAAGGACCACGTAGAAATGTCCCAAAGGACCACATAG
* * * * *
740103 ATATGTCCCG-AGGACCGCGTAGAAATGTCTCGAAGGACCACGTAG
1 ATATGTACCGAAGGACCACGTAGAAATGTCCCAAAGGACCACATAG
740148 A
1 A
740149 ATTTTTTCGA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
45 31 0.77
46 9 0.22
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (46 bp):
ATATGTACCGAAGGACCACGTAGAAATGTCCCAAAGGACCACATAG
Found at i:740291 original size:14 final size:14
Alignment explanation
Indices: 740272--740332 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
740262 TTATACCATT
740272 TCACATAGCTTATA
1 TCACATAGCTTATA
**
740286 TCACATAGACAAATA
1 TCACATAG-CTTATA
*
740301 TCACATAG---ATG
1 TCACATAGCTTATA
740312 TCACATAGCTTATA
1 TCACATAGCTTATA
740326 TCACATA
1 TCACATA
740333 TTCATATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 10 0.26
14 17 0.44
15 12 0.31
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (14 bp):
TCACATAGCTTATA
Found at i:740847 original size:19 final size:18
Alignment explanation
Indices: 740814--740864 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
740804 CTTCCTCATG
740814 GTATCAATA-ATTCTTCA
1 GTATCAATACATTCTTCA
740831 GTATCAATACTATTCTTCA
1 GTATCAATAC-ATTCTTCA
*
740850 GT-TCGATACCATTCT
1 GTATCAATA-CATTCT
740865 ACATTCTGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 9 0.30
18 10 0.33
19 11 0.37
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
GTATCAATACATTCTTCA
Found at i:740863 original size:18 final size:19
Alignment explanation
Indices: 740814--740864 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
740804 CTTCCTCATG
740814 GTATCAATA--ATTCTTCA
1 GTATCAATACCATTCTTCA
*
740831 GTATCAATACTATTCTTCA
1 GTATCAATACCATTCTTCA
*
740850 GT-TCGATACCATTCT
1 GTATCAATACCATTCT
740865 ACATTCTGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 9 0.30
18 11 0.37
19 10 0.33
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (19 bp):
GTATCAATACCATTCTTCA
Found at i:740927 original size:15 final size:15
Alignment explanation
Indices: 740907--740935 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
740897 CAATACTTGT
740907 CCATTGGTATCGATA
1 CCATTGGTATCGATA
740922 CCATTGGTATCGAT
1 CCATTGGTATCGAT
740936 GCTACTCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (15 bp):
CCATTGGTATCGATA
Found at i:744245 original size:60 final size:60
Alignment explanation
Indices: 744179--744296 Score: 218
Period size: 60 Copynumber: 2.0 Consensus size: 60
744169 GTTTTCCACA
*
744179 TAAATTTTGTGTCTTCTTTATCTTCATTTTTATTTTCTCAAATTATCAGTTGCGATTTCG
1 TAAATTTTGTGTCTTCTTTATCTTCATTTTTATTTTCTCAAATTATCAGTTACGATTTCG
*
744239 TAAATTTTGTGTCTTCTTTATCTTTATTTTTATTTTCTCAAATTATCAGTTACGATTT
1 TAAATTTTGTGTCTTCTTTATCTTCATTTTTATTTTCTCAAATTATCAGTTACGATTT
744297 TGCTCTATCT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.21, C:0.14, G:0.08, T:0.57
Consensus pattern (60 bp):
TAAATTTTGTGTCTTCTTTATCTTCATTTTTATTTTCTCAAATTATCAGTTACGATTTCG
Found at i:749624 original size:59 final size:59
Alignment explanation
Indices: 749479--749644 Score: 176
Period size: 59 Copynumber: 2.8 Consensus size: 59
749469 CATCTCTTTT
* * * * * * * *
749479 TAAATTGGTCTCTAAATTTTTAAATATTTCATTTTCATCCCTAGACTTTGACTATCATTT
1 TAAATTGGTCCCCAAATTTTTGAACATTTCAATTTCATCCC-AAACTATGACTATCATTC
** *
749539 TAAATTAATCCTCAAATTTTTGAACATTTCAATTTCA-CCCAAACTATGACCT-TCATTC
1 TAAATTGGTCCCCAAATTTTTGAACATTTCAATTTCATCCCAAACTATGA-CTATCATTC
*
749597 TAAATTGGTCCCCAAACTTTTTGAACATTCCAATTT-ATCCCAAACTAT
1 TAAATTGGTCCCCAAA-TTTTTGAACATTTCAATTTCATCCCAAACTAT
749645 ACGTATATAC
Statistics
Matches: 88, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
58 26 0.30
59 33 0.38
60 29 0.33
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (59 bp):
TAAATTGGTCCCCAAATTTTTGAACATTTCAATTTCATCCCAAACTATGACTATCATTC
Found at i:752114 original size:65 final size:62
Alignment explanation
Indices: 752037--752156 Score: 161
Period size: 65 Copynumber: 1.9 Consensus size: 62
752027 GAACGGTGTT
* * *
752037 GACCTGAACCCGATTTGGACCTGAAAATTATGGAT-CCGAACCCGACCTGCATCCGACCTGAGAA
1 GACCTGAACCCGAATTGAACC-GAAAA-TAT-GATACCGAACCCGAAC-GCATCCGACCTGAGAA
752101 C
62 C
752102 GACCTGAACCCGAATTGAACCGAAAATATGATACCCGAACCCGAACGCATCCGAC
1 GACCTGAACCCGAATTGAACCGAAAATATGATA-CCGAACCCGAACGCATCCGAC
752157 TGATATGAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
62 3 0.06
63 12 0.24
64 16 0.32
65 19 0.38
ACGTcount: A:0.33, C:0.32, G:0.20, T:0.16
Consensus pattern (62 bp):
GACCTGAACCCGAATTGAACCGAAAATATGATACCGAACCCGAACGCATCCGACCTGAGAAC
Found at i:752525 original size:23 final size:22
Alignment explanation
Indices: 752491--752538 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 22
752481 AATGCAAAGA
752491 AAATTAATATAGTTTTAATTATAT
1 AAATTAATATAG-TTTAATT-TAT
752515 AAATT-ATATAGTTTAATTTAT
1 AAATTAATATAGTTTAATTTAT
752536 AAA
1 AAA
752539 GAAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 6 0.25
22 7 0.29
23 6 0.25
24 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
AAATTAATATAGTTTAATTTAT
Found at i:752639 original size:23 final size:23
Alignment explanation
Indices: 752608--752656 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
752598 TTACATTAAT
*
752608 ATAAATAATTTTGGTAATAAAT-A
1 ATAAATAA-TTTGATAATAAATGA
*
752631 ATAATTAATTTGATAATAAATGA
1 ATAAATAATTTGATAATAAATGA
752654 ATA
1 ATA
752657 TTAGTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (23 bp):
ATAAATAATTTGATAATAAATGA
Found at i:752860 original size:10 final size:10
Alignment explanation
Indices: 752845--752876 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
752835 TGAATACAAT
752845 AAAATGAAAA
1 AAAATGAAAA
752855 AAAATG-AAA
1 AAAATGAAAA
752864 AAAATGAAAA
1 AAAATGAAAA
752874 AAA
1 AAA
752877 TTTAAGCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (10 bp):
AAAATGAAAA
Found at i:752864 original size:9 final size:9
Alignment explanation
Indices: 752845--752877 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
752835 TGAATACAAT
752845 AAAATGAAAA
1 AAAATG-AAA
752855 AAAATGAAA
1 AAAATGAAA
752864 AAAATGAAA
1 AAAATGAAA
752873 AAAAT
1 AAAAT
752878 TTAAGCTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (9 bp):
AAAATGAAA
Found at i:754351 original size:516 final size:511
Alignment explanation
Indices: 753382--754409 Score: 1900
Period size: 516 Copynumber: 2.0 Consensus size: 511
753372 TAATAAATAC
753382 AATAAGTAATTAAAAAGTAAAAGTTACCTGTAACAGAAGAAACAAGACTGAATCGTAAATTCGAA
1 AATAAGTAATTAAAAAGTAAAAGTTACCTGTAACAGAAGAAACAAGACTGAATCGTAAATTCGAA
753447 TGGCTTCACTTAACGTGAACACCCTAAAAAATTAAAATTAAAATAATTAATAAATAGTTTGAAAT
66 TGGCTTCACTTAACGTGAACACCCTAAAAAATTAAAATTAAAATAATTAATAAATAGTTTGAAAT
*
753512 ATTGAGATTAAAATAAAATATAAAAGCAATTGCATACCTTACATAGCAGAGTCATTAACCATAGT
131 ATTGAGATTAAAATAAAATATAAAAGCAATTGCATACCTTACATAGCAGAGTCATTAACCACAGT
753577 AAGGTAGTCTTATCCTTATCCTCCGGCTCAAAACCATACAACCAATTACGGGTTGTAACAAAAAT
196 AAGGTAGTCTTATCCTTATCCTCCGGCTCAAAACCATACAACCAATTACGGGTTGTAACAAAAAT
*
753642 CTCAACATTTTGGTAAGAGTGAAGCTCTTAATTTGGTCAAAATTCTACCCCCCATATAAAGGACG
261 CTCAACATTTTGGTAAGAGTGAAGCTCTTAATTTGGTCAAAATTCTACACCCCATATAAAGGACG
* *
753707 ATTCAGATGCAACGAAGTAATTCGAATAGCCAATATATCTCTCGCCATGCGAGAAAGTACATGAT
326 ATTCAGATGCAACGAAGTAATTCGAATAGACAATATATCTCTCGCCATGCGAGAAAGTACAGGAT
753772 ATGAAACACGTTGATTTTTCCAATACTCCAAAATATCAAAGTCTGATTCTCCAGTACGAGGGACA
391 ATGAAACACGTTGATTTTTCCAATACTCCAAAATATCAAAGTCTGATTCTCCAGTACGAGGGACA
*
753837 AGGGGTAAACTGATGTACGAGTCAACATCAGATCGTCCACTCCTTGAAGCAACTAA
456 AGGGGTAAACTAATGTACGAGTCAACATCAGATCGTCCACTCCTTGAAGCAACTAA
753893 AATAAGTAATTAAAAAGTAAAAGTTACCTGTAA-AGAA-AAACAAGACTGAATCGTAAATTCGAA
1 AATAAGTAATTAAAAAGTAAAAGTTACCTGTAACAGAAGAAACAAGACTGAATCGTAAATTCGAA
753956 TGGCTTCACTTAACGTGAACACCCTAAAAAATTAAAATTAAAATAATTAATAAATAGTTTGAAAT
66 TGGCTTCACTTAACGTGAACACCCTAAAAAATTAAAATTAAAATAATTAATAAATAGTTTGAAAT
* *
754021 ATTGATATTAAAATAAAATAT-AAAGCAATTATATCATACCTTTACATAGCAGAGTCATTAACCA
131 ATTGAGATTAAAATAAAATATAAAAGCAA-T-T-GCATACC-TTACATAGCAGAGTCATTAACCA
754085 CAGTAAGGTAGTCTTTATCCTTATCCTCCGGCTCAAAACCATACAACCAATTACGGGTTGTAACA
192 CAGTAAGGTAGTC-TTATCCTTATCCTCCGGCTCAAAACCATACAACCAATTACGGGTTGTAACA
754150 AAAATCTCAACATTTTTGGTAAGAGTGAAGCTCTTAATTTGGTCAAAATTCTACACCCCATACTA
256 AAAATCTCAACA-TTTTGGTAAGAGTGAAGCTCTTAATTTGGTCAAAATTCTACACCCCATA-TA
754215 AAGGACGATTCAGATGCAACTGAAGTAATTCGAATAGACAATATATCTCTCGCCATGCGAGAAAG
319 AAGGACGATTCAGATGCAAC-GAAGTAATTCGAATAGACAATATATCTCTCGCCATGCGAGAAAG
754280 TACAGGATATGAAACACGTTGATTTTTCCAATACTCCAAAATATCAAAGTCTGATTCTCCAGTAC
383 TACAGGATATGAAACACGTTGATTTTTCCAATACTCCAAAATATCAAAGTCTGATTCTCCAGTAC
754345 GAGGGACAAGGGGTAAACTAATGTACGAGTCAACATCAGATCGTCCACTCCTTGAAGCAACTAA
448 GAGGGACAAGGGGTAAACTAATGTACGAGTCAACATCAGATCGTCCACTCCTTGAAGCAACTAA
754409 A
1 A
754410 TTAGCATCAA
Statistics
Matches: 502, Mismatches: 7, Indels: 11
0.97 0.01 0.02
Matches are distributed among these distances:
508 7 0.01
509 112 0.22
510 5 0.01
511 39 0.08
512 35 0.07
513 63 0.13
514 48 0.10
515 22 0.04
516 171 0.34
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (511 bp):
AATAAGTAATTAAAAAGTAAAAGTTACCTGTAACAGAAGAAACAAGACTGAATCGTAAATTCGAA
TGGCTTCACTTAACGTGAACACCCTAAAAAATTAAAATTAAAATAATTAATAAATAGTTTGAAAT
ATTGAGATTAAAATAAAATATAAAAGCAATTGCATACCTTACATAGCAGAGTCATTAACCACAGT
AAGGTAGTCTTATCCTTATCCTCCGGCTCAAAACCATACAACCAATTACGGGTTGTAACAAAAAT
CTCAACATTTTGGTAAGAGTGAAGCTCTTAATTTGGTCAAAATTCTACACCCCATATAAAGGACG
ATTCAGATGCAACGAAGTAATTCGAATAGACAATATATCTCTCGCCATGCGAGAAAGTACAGGAT
ATGAAACACGTTGATTTTTCCAATACTCCAAAATATCAAAGTCTGATTCTCCAGTACGAGGGACA
AGGGGTAAACTAATGTACGAGTCAACATCAGATCGTCCACTCCTTGAAGCAACTAA
Found at i:756364 original size:17 final size:17
Alignment explanation
Indices: 756344--756376 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
756334 CCAACAACAC
756344 AAACAAATCAACAGTAT
1 AAACAAATCAACAGTAT
*
756361 AAACAAATTAACAGTA
1 AAACAAATCAACAGTA
756377 GCTAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.15, G:0.06, T:0.18
Consensus pattern (17 bp):
AAACAAATCAACAGTAT
Found at i:756367 original size:102 final size:102
Alignment explanation
Indices: 756148--756375 Score: 404
Period size: 102 Copynumber: 2.2 Consensus size: 102
756138 AATGAATAAC
756148 CAACAGTATCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAA
1 CAACAGTATCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAA
*
756213 AAGCAATCTGAATGAACAACCAACAACACAAACAAAT
66 AAGCAATCCGAATGAACAACCAACAACACAAACAAAT
* *
756250 CAACAGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGTAGCTAACAACCTTATAA
1 CAACAGTATCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAA
756315 AAGCAATCCGAATGAACAACCAACAACACAAACAAAT
66 AAGCAATCCGAATGAACAACCAACAACACAAACAAAT
**
756352 CAACAGTATAAACAAATT-AACAGT
1 CAACAGTATCTACAAATTAAACAGT
756376 AGCTAGAAAT
Statistics
Matches: 120, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 6 0.05
102 114 0.95
ACGTcount: A:0.50, C:0.19, G:0.09, T:0.21
Consensus pattern (102 bp):
CAACAGTATCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAA
AAGCAATCCGAATGAACAACCAACAACACAAACAAAT
Found at i:756681 original size:6 final size:6
Alignment explanation
Indices: 756651--756800 Score: 97
Period size: 6 Copynumber: 25.3 Consensus size: 6
756641 CAGTTTTGAA
* * * * ** * *
756651 TTTGGG TTAGGA TTTGGG TTCGGG TTTGGG TTCGAA TTCGGG TTCGGG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
* * ** * *
756699 -TTCGG TTCGGG TTCAGG TTCGGG TTTGGG -TTAGG TTTGGG TTTGGG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
* ** * * * *
756745 TTAGGG TTTGGG TTTTAG TTTGAG TTAGGG TTTGGT TTTAGG TTTGGG
1 TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG TTTGGG
756793 TTTGGG TT
1 TTTGGG TT
756801 CGGTTAGGGG
Statistics
Matches: 110, Mismatches: 32, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
5 7 0.06
6 103 0.94
ACGTcount: A:0.07, C:0.05, G:0.43, T:0.45
Consensus pattern (6 bp):
TTTGGG
Found at i:756709 original size:17 final size:17
Alignment explanation
Indices: 756667--756752 Score: 75
Period size: 17 Copynumber: 4.9 Consensus size: 17
756657 TTAGGATTTG
*
756667 GGTTCGGGTTTGGGTTC
1 GGTTCGGGTTAGGGTTC
* *
756684 GAATTCGGGTTCGGGTTC
1 G-GTTCGGGTTAGGGTTC
756702 GGTTCGGGTTCA-GGTTC
1 GGTTCGGGTT-AGGGTTC
* * *
756719 GGGTTTGGGTTAGGTTTG
1 -GGTTCGGGTTAGGGTTC
*
756737 GGTTTGGGTTAGGGTT
1 GGTTCGGGTTAGGGTT
756753 TGGGTTTTAG
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
17 30 0.53
18 27 0.47
ACGTcount: A:0.06, C:0.09, G:0.45, T:0.40
Consensus pattern (17 bp):
GGTTCGGGTTAGGGTTC
Found at i:756710 original size:29 final size:29
Alignment explanation
Indices: 756666--756740 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
756656 GTTAGGATTT
756666 GGGTTCGGGTTTGGGTTC-GAATTCGGGTTC
1 GGGTTC-GGTTTGGGTTCAG-ATTCGGGTTC
* * *
756696 GGGTTCGGTTCGGGTTCAGGTTCGGGTTT
1 GGGTTCGGTTTGGGTTCAGATTCGGGTTC
*
756725 GGGTTAGGTTTGGGTT
1 GGGTTCGGTTTGGGTT
756741 TGGGTTAGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 32 0.82
30 7 0.18
ACGTcount: A:0.05, C:0.11, G:0.45, T:0.39
Consensus pattern (29 bp):
GGGTTCGGTTTGGGTTCAGATTCGGGTTC
Found at i:756717 original size:23 final size:23
Alignment explanation
Indices: 756667--756723 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
756657 TTAGGATTTG
* *
756667 GGTTCGGGTTTGGGTTCGAATTCG
1 GGTTCGGG-TTCGGTTCGAATTCA
**
756691 GGTTCGGGTTCGGTTCGGGTTCA
1 GGTTCGGGTTCGGTTCGAATTCA
756714 GGTTCGGGTT
1 GGTTCGGGTT
756724 TGGGTTAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.72
24 8 0.28
ACGTcount: A:0.05, C:0.14, G:0.44, T:0.37
Consensus pattern (23 bp):
GGTTCGGGTTCGGTTCGAATTCA
Found at i:756812 original size:19 final size:21
Alignment explanation
Indices: 756790--756830 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
756780 TTTTAGGTTT
*
756790 GGGTTTGGGTTC-GG-TTAGG
1 GGGTTCGGGTTCTGGTTTAGG
756809 GGGTTCGGGTTCTGGTTTAGG
1 GGGTTCGGGTTCTGGTTTAGG
756830 G
1 G
756831 TTCAAGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 2 0.11
21 6 0.32
ACGTcount: A:0.05, C:0.07, G:0.51, T:0.37
Consensus pattern (21 bp):
GGGTTCGGGTTCTGGTTTAGG
Found at i:757139 original size:10 final size:10
Alignment explanation
Indices: 757124--757150 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
757114 GAGGTTTTTC
757124 GGATGAACAA
1 GGATGAACAA
757134 GGATGAACAA
1 GGATGAACAA
757144 GGATGAA
1 GGATGAA
757151 AATTTCGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.07, G:0.33, T:0.11
Consensus pattern (10 bp):
GGATGAACAA
Found at i:757684 original size:27 final size:27
Alignment explanation
Indices: 757639--757739 Score: 78
Period size: 32 Copynumber: 3.4 Consensus size: 27
757629 ATAATTAACT
*
757639 ATTAATAATAATAAATAATTATATTATA
1 ATTAAT-ATAATAATTAATTATATTATA
*
757667 ATTAATATAATAATTAATATTAAATTAATTA
1 ATTAATATAATAATT-A-ATTATATT-A-TA
* *
757698 TATTAATATAATATAGTTTATAAT-TTATA
1 -ATTAATATAATA-A-TTAATTATATTATA
757727 ATTAATATTAATA
1 ATTAATA-TAATA
757740 TAAAATATAG
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
27 8 0.13
28 14 0.23
29 14 0.23
30 2 0.03
31 4 0.07
32 15 0.25
33 1 0.02
34 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (27 bp):
ATTAATATAATAATTAATTATATTATA
Found at i:757699 original size:24 final size:24
Alignment explanation
Indices: 757629--757711 Score: 84
Period size: 24 Copynumber: 3.5 Consensus size: 24
757619 ATATATTTTT
*
757629 ATAATTAACTATT-AA-TAATAATAA
1 ATAATTAA-TATTAAATTAATTAT-A
757653 ATAATT-ATATTATAATTAA-TATA
1 ATAATTAATATTA-AATTAATTATA
757676 ATAATTAATATTAAATTAATTATA
1 ATAATTAATATTAAATTAATTATA
*
757700 TTAATATAATAT
1 ATAAT-TAATAT
757712 AGTTTATAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
22 4 0.08
23 14 0.27
24 24 0.47
25 9 0.18
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (24 bp):
ATAATTAATATTAAATTAATTATA
Found at i:757709 original size:14 final size:14
Alignment explanation
Indices: 757676--757892 Score: 56
Period size: 15 Copynumber: 14.5 Consensus size: 14
757666 AATTAATATA
757676 ATAATTAATATTAA-
1 ATAATT-ATATTAAT
757690 ATTAATTATATTAAT
1 A-TAATTATATTAAT
*
757705 ATAATATAGTTTATAATTT
1 ATAAT-TA-TAT-TAA--T
757724 ATAATTAATATTAAT
1 ATAATT-ATATTAAT
*
757739 ATAAAATATAGTCT-AT
1 AT-AATTATA-T-TAAT
757755 A-ACATTAATATTAAT
1 ATA-ATT-ATATTAAT
*
757770 ATAAATTATATGTTAT
1 AT-AATTATAT-TAAT
*
757786 A-AATTATA-TAGT
1 ATAATTATATTAAT
* *
757798 AT-ATTTTATAAACT
1 ATAATTATATTAA-T
* *
757812 ATAGTTAATATAAAT
1 ATAATT-ATATTAAT
757827 A-ATATTAGTA-TAAT
1 ATA-ATTA-TATTAAT
* *
757841 ATAGTT-TATAAACT
1 ATAATTATATTAA-T
*
757855 ATATACTATATTAAT
1 ATA-ATTATATTAAT
*
757870 ATAAATTATAGTTAAG
1 AT-AATTATA-TTAAT
757886 ATAATTA
1 ATAATTA
757893 AACATATAAA
Statistics
Matches: 151, Mismatches: 21, Indels: 61
0.65 0.09 0.26
Matches are distributed among these distances:
12 10 0.07
13 3 0.02
14 36 0.24
15 47 0.31
16 37 0.25
17 8 0.05
18 3 0.02
19 7 0.05
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (14 bp):
ATAATTATATTAAT
Found at i:757765 original size:31 final size:30
Alignment explanation
Indices: 757722--757791 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 30
757712 AGTTTATAAT
757722 TTAT-AATTAATATTAATATAAAATATA-G
1 TTATAAATTAATATTAATATAAAATATATG
*
757750 TCTATAACATTAATATTAATATAAATTATATG
1 T-TATAA-ATTAATATTAATATAAAATATATG
757782 TTATAAATTA
1 TTATAAATTA
757792 TATAGTATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 1 0.03
29 3 0.08
30 5 0.14
31 26 0.70
32 2 0.05
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (30 bp):
TTATAAATTAATATTAATATAAAATATATG
Found at i:758081 original size:17 final size:18
Alignment explanation
Indices: 758049--758092 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 18
758039 TGTATATTAC
758049 ATATACTATAGGTTATAT
1 ATATACTATAGGTTATAT
758067 ATATAC-ATA-GTT-TAT
1 ATATACTATAGGTTATAT
*
758082 ATACACTATAG
1 ATATACTATAG
758093 ATAGTTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 8 0.35
16 6 0.26
17 3 0.13
18 6 0.26
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (18 bp):
ATATACTATAGGTTATAT
Found at i:758145 original size:35 final size:37
Alignment explanation
Indices: 758105--758173 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 37
758095 AGTTTATACA
*
758105 TACATGATACATGTACTATAAGTT-CA-TATATAGTT
1 TACATGATACATATACTATAAGTTACATTATATAGTT
* *
758140 TACATGTTACATATACTATAGGTTACATTATATA
1 TACATGATACATATACTATAAGTTACATTATATA
758174 TATTAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 21 0.72
36 2 0.07
37 6 0.21
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.41
Consensus pattern (37 bp):
TACATGATACATATACTATAAGTTACATTATATAGTT
Found at i:758192 original size:7 final size:7
Alignment explanation
Indices: 758184--758249 Score: 64
Period size: 7 Copynumber: 9.7 Consensus size: 7
758174 TATTAATTAT
*
758184 GGTTTAT
1 GGTTTAG
758191 GGTTTAG
1 GGTTTAG
758198 GGTTTAG
1 GGTTTAG
*
758205 AGTTTA-
1 GGTTTAG
* *
758211 TGTTTAA
1 GGTTTAG
* *
758218 AG-TTAT
1 GGTTTAG
758224 GGTTTAG
1 GGTTTAG
758231 GGTTTAG
1 GGTTTAG
758238 GGTTTAG
1 GGTTTAG
758245 GGTTT
1 GGTTT
758250 TATAAACTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
6 9 0.18
7 41 0.82
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.48
Consensus pattern (7 bp):
GGTTTAG
Found at i:758203 original size:14 final size:14
Alignment explanation
Indices: 758180--758249 Score: 72
Period size: 14 Copynumber: 5.1 Consensus size: 14
758170 TATATATTAA
*
758180 TTATGGTTTATGGT
1 TTATGGTTTAGGGT
* *
758194 TTAGGGTTTAGAGT
1 TTATGGTTTAGGGT
**
758208 TTAT-GTTTAAAG-
1 TTATGGTTTAGGGT
758220 TTATGGTTTAGGGT
1 TTATGGTTTAGGGT
*
758234 TTAGGGTTTAGGGT
1 TTATGGTTTAGGGT
758248 TT
1 TT
758250 TATAAACTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
12 4 0.09
13 13 0.28
14 29 0.63
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (14 bp):
TTATGGTTTAGGGT
Found at i:758692 original size:25 final size:24
Alignment explanation
Indices: 758623--758692 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 24
758613 TTTTCTTTAA
* * *
758623 TATATATATATACT-TATATTAGT
1 TATACATATATACTATATATAAAT
758646 TATACATATATACTATTAATATAAAT
1 TATACATATATACTA-T-ATATAAAT
*
758672 TATAACATATAAACTATATAT
1 TAT-ACATATATACTATATAT
758693 TTTATAGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 13 0.33
25 5 0.13
26 10 0.26
27 11 0.28
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.44
Consensus pattern (24 bp):
TATACATATATACTATATATAAAT
Found at i:758713 original size:13 final size:13
Alignment explanation
Indices: 758695--758724 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
758685 CTATATATTT
758695 TATAGTTTATACA
1 TATAGTTTATACA
*
758708 TATAGTTTATATA
1 TATAGTTTATACA
758721 TATA
1 TATA
758725 TATACTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (13 bp):
TATAGTTTATACA
Found at i:758791 original size:73 final size:70
Alignment explanation
Indices: 758646--758780 Score: 180
Period size: 73 Copynumber: 1.9 Consensus size: 70
758636 TTATATTAGT
*
758646 TATACATATATACTATTAATATAAATTATAACATATAAACTATATATTTTATAGTTTATACATAT
1 TATACATATATACTATTAATATAAATAATAACATATAAACTATATATTTTATAGTTTATA-ATAT
758711 AGTTTA
65 AGTTTA
* ***
758717 TATATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTTTTATAGTTTATA
1 TATACATATATAC--TATTAATATAAATAATAACATATAAACTATATA--TTTTATAGTTTATA
758781 TACTTTTTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
71 12 0.22
73 29 0.53
75 14 0.25
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.47
Consensus pattern (70 bp):
TATACATATATACTATTAATATAAATAATAACATATAAACTATATATTTTATAGTTTATAATATA
GTTTA
Found at i:758796 original size:18 final size:18
Alignment explanation
Indices: 758749--758798 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
758739 ATAAATAATA
**
758749 TTTTATAAACTATATACT
1 TTTTATAATTTATATACT
*
758767 TTTTATAGTTTATATACT
1 TTTTATAATTTATATACT
758785 TTTTATAATTTATA
1 TTTTATAATTTATA
758799 CATAATAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTTATAATTTATATACT
Found at i:758917 original size:13 final size:13
Alignment explanation
Indices: 758901--758981 Score: 58
Period size: 13 Copynumber: 5.9 Consensus size: 13
758891 AGTTTATAAT
*
758901 TTTATATACATAG
1 TTTATATATATAG
758914 TTTATATATATAG
1 TTTATATATATAG
* * *
758927 TTCACATAAATATAA
1 TT--TATATATATAG
758942 TTTATATA-ATAG
1 TTTATATATATAG
758954 TTTATAATAATTATTAG
1 TTTAT-AT-A-TA-TAG
758971 TTTATA-ATATA
1 TTTATATATATA
758982 AATATAATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
12 10 0.19
13 22 0.41
14 2 0.04
15 10 0.19
16 2 0.04
17 8 0.15
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (13 bp):
TTTATATATATAG
Found at i:758921 original size:96 final size:98
Alignment explanation
Indices: 758809--759006 Score: 312
Period size: 96 Copynumber: 2.0 Consensus size: 98
758799 CATAATAGTT
* *
758809 TATACATAGTTTATATATATAGTTCACATAAACATAATTTA-ATTATAGCTTATGATAATTATAT
1 TATACATAGTTTATATATATAGTTCACATAAACATAATTTATATAATAGCTTATAATAATTAT-T
758873 AGTTTATAATATAAATAT-AGTT-TATAATTTTA
65 AGTTTATAATATAAATATAAGTTATATAATTTTA
* *
758905 TATACATAGTTTATATATATAGTTCACATAAATATAATTTATATAATAGTTTATAATAATTATTA
1 TATACATAGTTTATATATATAGTTCACATAAACATAATTTATATAATAGCTTATAATAATTATTA
*
758970 GTTTATAATATAAATATAATTTAATATAATTTTA
66 GTTTATAATATAAATATAAGTT-ATATAATTTTA
759004 TAT
1 TAT
759007 TATATATATT
Statistics
Matches: 93, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
96 59 0.63
97 21 0.23
99 13 0.14
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (98 bp):
TATACATAGTTTATATATATAGTTCACATAAACATAATTTATATAATAGCTTATAATAATTATTA
GTTTATAATATAAATATAAGTTATATAATTTTA
Found at i:758989 original size:47 final size:48
Alignment explanation
Indices: 758836--758999 Score: 142
Period size: 47 Copynumber: 3.4 Consensus size: 48
758826 TATAGTTCAC
* * * *
758836 ATAAACATAATTTA-ATTATAGCTTATGATAATTATATAGTTTATAAT
1 ATAAATATAATTTATATAATAGTTTATAATAATTATATAGTTTATAAT
* * * * * *
758883 ATAAATAT-AGTT-TATAAT-TTTATATACATAGTTTATATA-TATAGTTCAC
1 ATAAATATAATTTATATAATAGTT-TATA-ATA-ATTATATAGTTTA--TAAT
758932 ATAAATATAATTTATATAATAGTTTATAATAATTAT-TAGTTTATAAT
1 ATAAATATAATTTATATAATAGTTTATAATAATTATATAGTTTATAAT
758979 ATAAATATAATTTAATATAAT
1 ATAAATATAATTT-ATATAAT
759000 TTTATATTAT
Statistics
Matches: 90, Mismatches: 16, Indels: 21
0.71 0.13 0.17
Matches are distributed among these distances:
45 1 0.01
46 10 0.11
47 28 0.31
48 16 0.18
49 17 0.19
50 6 0.07
51 10 0.11
52 2 0.02
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (48 bp):
ATAAATATAATTTATATAATAGTTTATAATAATTATATAGTTTATAAT
Found at i:761139 original size:10 final size:9
Alignment explanation
Indices: 761114--761138 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
761104 TATTTTATGT
761114 TGTTTTTAC
1 TGTTTTTAC
761123 TGTTTTTAC
1 TGTTTTTAC
761132 TGTTTTT
1 TGTTTTT
761139 TTTATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.08, G:0.12, T:0.72
Consensus pattern (9 bp):
TGTTTTTAC
Found at i:764073 original size:31 final size:29
Alignment explanation
Indices: 764013--764074 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
764003 ATTTGGCGTA
*
764013 ATACATAAATTTTAATTTATTGTAATTAT
1 ATACAAAAATTTTAATTTATTGTAATTAT
764042 ATACAAAATATTTTAATTTTAATT-TAATTAT
1 ATACAAAA-ATTTTAA-TTT-ATTGTAATTAT
764073 AT
1 AT
764075 GTAGTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.24
30 7 0.24
31 12 0.41
32 3 0.10
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (29 bp):
ATACAAAAATTTTAATTTATTGTAATTAT
Done.